Faster Phylogenetic Inference with MXG
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- Mitchell D.G., Hach F., Mohebali R. (2007) Faster Phylogenetic Inference with MXG. In: Dershowitz N., Voronkov A. (eds) Logic for Programming, Artificial Intelligence, and Reasoning. LPAR 2007. Lecture Notes in Computer Science, vol 4790. Springer, Berlin, Heidelberg
We apply the logic-based declarative programming approach of Model Expansion (MX) to a phylogenetic inference task. We axiomatize the task in multi-sorted first-order logic with cardinality constraints. Using the model expansion solver MXG and SAT+cardinality solver MXC, we compare the performance of several MX axiomatizations on a challenging set of test instances. Our methods perform orders of magnitude faster than previously reported declarative solutions. Our best solution involves polynomial-time pre-processing, redundant axioms, and symmetry-breaking axioms. We also discuss our method of test instance generation, and the role of pre-processing in declarative programming.
KeywordsPhylogeny Declarative Programming Model Expansion
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